Is this the latest version of gradunwarp? What python are you using? Matt.
From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Anthony Dick <ad...@fiu.edu<mailto:ad...@fiu.edu>> Date: Thursday, November 15, 2018 at 8:49 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Problem with gradunwarp Hello! We have been trying to use gradunwarp on Siemens Prisma diffusion data (we’re using: https://github.com/Washington-University/gradunwarp). We have encountered what appears to be the same problem as described here: https://www.mail-archive.com/hcp-users@humanconnectome.org/msg01679.html However, it is not clear how this was resolved (an email to the poster suggests it may not have been). We’re looking for either a solution to this issue, or suggestions for alternative programs to achieve the same goal (preferably not matlab). Here is a complete screen-dump of the error: (/home/data/nbc/data-analysis/env3) -bash-4.1$ gradient_unwarp.py /home/data/dcnlab/AHEAD/sub-4150318/ses-S1/dwi/sub-4150318_ses-S1_run-01_dwi.nii.gz /home/data/dcnlab/AHEAD/sub-4150318/ses-S1/dwi/sub-4150318_ses-S1_run-01_desc-unwarp_dwi.nii.gz siemens -g /home/data/dcnlab/AHEAD/coeff.grad -n gradunwarp-INFO: Parsing /home/data/dcnlab/AHEAD/coeff.grad for harmonics coeffs gradunwarp-INFO: Evaluating spherical harmonics gradunwarp-INFO: on a 60^3 grid gradunwarp-INFO: with extents -300.0mm to 300.0mm gradunwarp-INFO: along x... gradunwarp-INFO: along y... gradunwarp-INFO: along z... gradunwarp-INFO: Evaluating the jacobian multiplier gradunwarp-INFO: Unwarping slice by slice . Traceback (most recent call last): File "/home/data/nbc/data-analysis/env3/bin/gradient_unwarp.py", line 122, in <module> grad_unwarp.run() File "/home/data/nbc/data-analysis/env3/bin/gradient_unwarp.py", line 111, in run self.unwarper.run() File "/home/data/nbc/data-analysis/env3/lib/python3.6/site-packages/gradunwarp/core/unwarp_resample.py", line 154, in run m_rcs2lai, m_rcs2lai_nohalf, g_xyz2rcs) File "/home/data/nbc/data-analysis/env3/lib/python3.6/site-packages/gradunwarp/core/unwarp_resample.py", line 274, in non_linear_unwarp_siemens order=self.order) File "/home/data/nbc/data-analysis/env3/lib/python3.6/site-packages/scipy/ndimage/interpolation.py", line 319, in map_coordinates raise RuntimeError('invalid shape for coordinate array') RuntimeError: invalid shape for coordinate array (/home/data/nbc/data-analysis/env3) -bash-4.1$ Thanks for any help, Anthony -- Anthony Steven Dick, Ph.D. Associate Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Florida International University MM Campus AHC4 454 Department of Psychology and Center for Children and Families<http://www.ccf.fiu.edu/>, an FIU Preeminent Program<https://beyondpossible.fiu.edu/preeminent-programs/> 11200 S.W. 8th Street Miami, FL 33199 Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 Email: ad...@fiu.edu<mailto:ad...@fiu.edu>; Webpage: http://dcn.fiu.edu<http://dcn.fiu.edu/>; Join the SSHD<http://www.sshdonline.org/> ##### Check out the new book<http://www.routledge.com/9781138960039>: Dick, A.S., & Müller, U. (2018). Advancing Developmental Science: Philosophy, Theory, and Method. Taylor & Francis. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
